In terms of the core query here: I don't think a shift needs to be made with regard to enchant containers. Why? Because they also do seed in stash rooms. And you'll pick them up naturally as you're busy doing other things (missions, etc), too. They are like coins in mario, they are all over the place. If you want to go somewhere specific and grind them, then you can -- hooray. But if you don't, the game doesn't force you, and you'll still have a healthy dose of them in no time.
In short, I think it works as well as coins do in mario, or any other sort of minor collectible sort of thing that leads to a major reward. Unless you are the sort who never almost dies in mario (ahem), collecting coins could be considered semi-optional at best, because those are your primary means to getting 1ups unless you know some specific way to grind 1ups like the turtle-on-stairs trick in SMB1, for instance. And if you know (and can execute) that trick, you probably already don't need the lives.
I could not be happier with how it's playing out at the moment, with regards to enchant rates and how frequent you get the containers, to be perfectly honest. It's not the core focus of the game, but it's always something that is there, and it's exciting when you get more, and you can choose to accelerate that process or not. It serves much the same sort of psychological role as EXP does in many other games, without actually being EXP.